November 2007

November 30, 2007

To minimize the time when the stats is updating, we're going to try out updating it every 2 hours instead of every hour. The idea is that the time to input the stats won't be that much longer (due to various overheads), so there will be more time that the stats are available.

We've also been making some tweaks to the stats pages to make it higher performance. If that looks good, we could go back to allowing for simultaneous db access during updates (which we used to do about a year ago).

Jason Wagoner is a relatively new member of the FAH team, but has already made some critically important contributions. Jason has already done a great deal of research relevant to Folding@home, when he was an undergraduate at Washington University at St Louis, working in Nathan Baker's lab. Jason's work centers around understanding water, and how water interacts with proteins. In particular, Jason is an expert in developing models for water which (we hope) will be more accurate, faster than existing models, AND well suited to architectures such as the PS3 or GPU. Jason has been working with Dr. Edgar Luttmann (see previous post about Edgar) on this new water model, and we're hoping to have our first paper submitted for peer review soon (maybe 1-2 weeks).

November 28, 2007

Since the forum is taking a while, we (Stanford + mods) have decided that it's best to have something until the new forum is up, so let's use Google groups for now. This is non-ideal, but better than nothing.

There have been many questions regarding the forum and I want to give an update. WW is still working to get the old one up, but we are working in parallel to get a backup/replacement perhaps at Stanford. Both efforts have hit a few snags, but work is on going.

The mods have been monitoring team forums to try to help out until the main forum comes back. We are considering something like yahoo or google groups as a temporary place to go until either of the options mentioned above gets going.

November 24, 2007

The forum has been down for a few days. WW has had it with his hosting company and tells me that he is moving the server to another vendor to improve the major reliability problems we have been seeing. There is no ETA for the forum coming back, but we're expecting it to be relatively soon. If it takes too long, we can use a forum we've set up at Stanford to serve the folding community.

November 23, 2007

Since Thursday was Thanksgiving in the US -- a day when one eats lots of Turkey -- I can't resist talking about turkey and tryptophan. Every one knows what a turkey is, and actually many people have heard that tryptophan is the compound in turkey that makes one sleepy, but what is tryptophan?

Tryptophan is an amino acid -- one of the 20 amino acids commonly found in proteins in fact. The chemical structure of tryptophan (or Trp as it is abbreviated -- spoken as "Trip") is shown in the right. It turns out that Trp is one of the most bulky amino acids, with its ring structure. Being a bulky ring, Trp is one of the most hydrophobic amino acids, and is thus present in protein cores.

Moreover, Trp has a very important properties in the study of protein folding. Due to its ring structure, Trp fluoresces (i.e. gives off light at a particular frequency, when hit with light of another frequency), and so Trp is a very important probe of protein folding. When a protein is unfolded, usually its Trp residues are exposed to solvent, but when folded, Trp is buried. This difference leads to differences in how it fluoresces, which can be measured very precisely.

Finally, it's interesting to ask where does Trp come from? Most animals can't make Trp on their own and instead get it from plants, but where do plants get Trp? Many plants can make it themselves, using an enzyme called Trp Synthase (shown on the right). As with all enzymes, Trp Synthase is itself a protein, so we have proteins synthesizing amino acids, which are used to build proteins!

November 22, 2007

It's Thanksgiving Day in the US -- a holiday where we eat a lot food, play some football, and most importantly think about the previous year and everything we've been grateful for. The FAH team at Stanford has lots to be thankful for over the last year, with the great turn out from FAH donors and new ports. We're even more excited about 2008, as we have done a lot of work this year to set up some new surprises for 2008 (and it will likely be in 2008 that some of our achievements in 2007, like the PS3 and GPU clients, really shine). Finally, we've had a strong year in terms of producing scientific results from FAH (check out our results page for details).

Anyway, from all of us on the FAH team, thanks to all the donors who make our work possible!

The forum is down again. Forum moderators are working to get it up ASAP, and we are in close contact with them. We have also been working to setup a backup site and we may engage that as needed. We will post updates here. One confounding problem is that this week is Thanksgiving week, with much of the US on holiday, but we'll make a push to get something going ASAP.

We have another new paper to come out in the Journal of Molecular Biology (paper #53 on our results web page). This paper is on protein folding and is Dan Ensign's first paper as lead author. It's also one of the first key results from the SMP client (I'm sure people feel like the SMP client has been out for quite a while, but this was actually a pretty fast turnaround, as analyzing the data, writing the paper, getting past peer review, and then getting published can easily take 12-24 months).

Dan wrote a nice non-technical summary of the paper which I'll include here:

This paper describes the first set of results
generated using the SMP clients. The main advantage of using SMP for
these sorts of calculations is that the amount of computation that one
client can do is several times larger than the traditional clients.
This means that our simulations can get many times longer that before;
in fact, this has allowed us to generate several hundred folding
trajectories of the fastest-folding protein known, the HP35-NleNle
variant of the villin headpiece subdomain. In this paper, because our
simulation time scales compare well to the 700-nanosecond experimental
folding time of this protein, AND we've generated enough trajectories
to get good statistics, we can shed some light on the experimental
results. To summarize the result, the first helix of the protein was
thought to be highly structured in the unfolded state of the protein;
we've suggested that structure in this part of the molecule is not
enough to lead to fast folding, and that longer time scales than the
700-ns mark may be present in this system.

Check out the movie: it shows some simulation we did
for this work, although watching one trajectory is emphatically NOT
statistically significant, which is the whole point of the paper! The movie is from a DL.tv interview I did and the main part I want to draw people's attention to is the movie of the protein folding simulation -- that simulation was from the SMP client and from the data set discussed in this paper.